At present, the reserves of most mining enterprises under the original industrial indexes are rapidly consumed, and the full use of low-grade resources is getting more and more attention. If mining enterprises want to make full use of low-grade resources and obtain good economic benefits simultaneously, it is necessary to strengthen the analysis and management of costs. For metal underground mines, with the gradual implementation of exploration and mining projects, capital investment and labor consumption are dynamic and increase cumulatively by stages. Consequently, in the evaluation of ore value, we should proceed from a series of processes such as exploration, mining, processing and smelting of geological resources, and then study the resources increment in different stages of production and processing. Based on the value chain theory, the analysis framework of gold mining enterprise value chain is established based on the value chain theory from the three dimensions of value-added activities, value subjects and value carriers. A value chain model using ore flow as the carrying body is built based on Petri nets. With the CPN Tools emulation tool, the cycle simulation of the model is realized by the colored Petri nets, which contain a hierarchical structure. Taking a large-scale gold mining enterprise as an example, the value chain model is quantified to simulate the ore value formation, flow, transmission and implementation process. By analyzing the results of the simulation, the ore value at different production stages is evaluated dynamically, and the cost is similarly analyzed in stages, which can improve mining enterprise cost management and provide the basis for effective utilization of low-grade ores.